User blog comment:MovesLikeZaki/Help Me Please/@comment-30155146-20171021154307

You probably are looking at  box 13 or another box with a high number.

In the box tab, scroll up in the box column and you should see the box that your pokemon are stored in.

If you want to get replacement pokemon, please send a screenshot of changes to every box in your PC, then send a photo and whatever happened before to a developer so the bug can be fixed.